6HRB

Cryo-EM structure of the KdpFABC complex in an E2 inward-facing state (state 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structures of KdpFABC suggest a K+transport mechanism via two inter-subunit half-channels.

Stock, C.Hielkema, L.Tascon, I.Wunnicke, D.Oostergetel, G.T.Azkargorta, M.Paulino, C.Hanelt, I.

(2018) Nat Commun 9: 4971-4971

  • DOI: 10.1038/s41467-018-07319-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K <sup>+ </sup> uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K ...

    P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K + uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K + has been assumed to be transported by the channel-like subunit KdpA. A first crystal structure uncovered its overall topology, suggesting such a spatial separation of energizing and transporting units. Here, we report two cryo-EM structures of the 157 kDa, asymmetric KdpFABC complex at 3.7 Å and 4.0 Å resolution in an E1 and an E2 state, respectively. Unexpectedly, the structures suggest a translocation pathway through two half-channels along KdpA and KdpB, uniting the alternating-access mechanism of actively pumping P-type ATPases with the high affinity and selectivity of K + channels. This way, KdpFABC would function as a true chimeric complex, synergizing the best features of otherwise separately evolved transport mechanisms.


    Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany.,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt/Main, Germany. haenelt@biochem.uni-frankfurt.de.,Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. c.paulino@rug.nl.,Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain.,Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase potassium-binding subunit
A
557Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: kdpA
Find proteins for P03959 (Escherichia coli (strain K12))
Go to UniProtKB:  P03959
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase ATP-binding subunit
B
682Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: kdpB
EC: 7.2.2.6
Find proteins for P03960 (Escherichia coli (strain K12))
Go to UniProtKB:  P03960
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase KdpC subunit
C
190Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: kdpC
Find proteins for P03961 (Escherichia coli (strain K12))
Go to UniProtKB:  P03961
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Potassium-transporting ATPase KdpF subunit
D
29Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: kdpF
Find proteins for P36937 (Escherichia coli (strain K12))
Go to UniProtKB:  P36937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyHA 6322/3-1
Netherlands Organisation for Scientific ResearchNetherlands722.017.001
European Research CouncilNetherlands749732

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-12-11
    Type: Other